Optimize code to read text-file with digits

Previous Topic Next Topic
 
classic Classic list List threaded Threaded
10 messages Options
Reply | Threaded
Open this post in threaded view
|

Optimize code to read text-file with digits

Martin Møller Skarbiniks Pedersen
Hi,

  Every day I try to write some small R programs to improve my R-skills.
  Yesterday I wrote a small program to read the digits from "A Million
Random Digits" from RAND.
  My code works but it is very slow and I guess the code is not optimal.

The digits.txt file downloaded from
https://www.rand.org/pubs/monograph_reports/MR1418.html
contains 20000 lines which looks like this:
00000   10097 32533  76520 13586  34673 54876  80959 09117  39292 74945
00001   37542 04805  64894 74296  24805 24037  20636 10402  00822 91665
00002   08422 68953  19645 09303  23209 02560  15953 34764  35080 33606
00003   99019 02529  09376 70715  38311 31165  88676 74397  04436 27659
00004   12807 99970  80157 36147  64032 36653  98951 16877  12171 76833

My program which is slow looks like this:

filename <- "digits.txt"
lines <- readLines(filename)

numbers <- vector('numeric')
for (i in 1:length(lines)) {

    # remove first column
    lines[i] <- sub("[^ ]+ +","",lines[i])

    # remove spaces
    lines[i] <- gsub(" ","",lines[i])

    # split the characters and convert them into numbers
    numbers <- c(numbers,as.numeric(unlist(strsplit(lines[i],""))))
}

Thanks for any advice how this program can be improved.

Regards
Martin M. S. Pedersen

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: Optimize code to read text-file with digits

PIKAL Petr
Hi

see in line

> -----Original Message-----
> From: R-help [mailto:[hidden email]] On Behalf Of Martin
> Moller Skarbiniks Pedersen
> Sent: Friday, September 8, 2017 10:49 AM
> To: [hidden email]
> Subject: [R] Optimize code to read text-file with digits
>
> Hi,
>
>   Every day I try to write some small R programs to improve my R-skills.
>   Yesterday I wrote a small program to read the digits from "A Million Random
> Digits" from RAND.
>   My code works but it is very slow and I guess the code is not optimal.
>
> The digits.txt file downloaded from
> https://www.rand.org/pubs/monograph_reports/MR1418.html
> contains 20000 lines which looks like this:
> 00000   10097 32533  76520 13586  34673 54876  80959 09117  39292 74945
> 00001   37542 04805  64894 74296  24805 24037  20636 10402  00822 91665
> 00002   08422 68953  19645 09303  23209 02560  15953 34764  35080 33606
> 00003   99019 02529  09376 70715  38311 31165  88676 74397  04436 27659
> 00004   12807 99970  80157 36147  64032 36653  98951 16877  12171 76833
>
> My program which is slow looks like this:
>
> filename <- "digits.txt"
> lines <- readLines(filename)

why you do not read a file as a whole e.g. by

lines<-read.table("digits.txt")

After that you do not need for cycle (but maybe I misunderstand what you really want)

remove first column

lines <- lines[,-1]

And now I am lost.
Do you want each row convert into a numeric vector? It probably exceed the precision of biggest number allowed.

Do you want to split each column to 5 numeric columns?
you can use something like

outer(lines[,1], 10^c(4:0), function(a, b) a %/% b %% 10)

to split the first column.

Or do you want one big numeric vector from all your numbers?

here you need to read values as character variables

lines<-read.table("digits.txt", colClasses="character")
numbers<-as.numeric(unlist(strsplit(as.character(lines[1,]),"")))
changes first row to numeric vector.

Anyway, can you explain what is your final goal?

Cheers
Petr


>
> numbers <- vector('numeric')
> for (i in 1:length(lines)) {
>
>     # remove first column
>     lines[i] <- sub("[^ ]+ +","",lines[i])
>
>     # remove spaces
>     lines[i] <- gsub(" ","",lines[i])
>
>     # split the characters and convert them into numbers
>     numbers <- c(numbers,as.numeric(unlist(strsplit(lines[i],""))))
> }
>
> Thanks for any advice how this program can be improved.
>
> Regards
> Martin M. S. Pedersen
>
>       [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

________________________________
Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny pouze jeho adresátům.
Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze svého systému.
Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat.
Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či zpožděním přenosu e-mailu.

V případě, že je tento e-mail součástí obchodního jednání:
- vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu.
- a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce s dodatkem či odchylkou.
- trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným dosažením shody na všech jejích náležitostech.
- odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi či osobě jím zastoupené známá.

This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients.
If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system.
If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner.
The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email.

In case that this e-mail forms part of business dealings:
- the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning.
- if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation.
- the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects.
- the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by the recipient.
______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: Optimize code to read text-file with digits

Martin Møller Skarbiniks Pedersen
On 8 September 2017 at 11:25, PIKAL Petr <[hidden email]> wrote:

> > Moller Skarbiniks Pedersen

> My program which is slow looks like this:
> >
> > filename <- "digits.txt"
> > lines <- readLines(filename)
>
> why you do not read a file as a whole e.g. by
>
> lines<-read.table("digits.txt")
>

Good idea.

>
> And now I am lost.


[...]


>  Or do you want one big numeric vector from all your numbers?

here you need to read values as character variables
>

Yes. That's what I am looking for.

>
> lines<-read.table("digits.txt", colClasses="character")
> numbers<-as.numeric(unlist(strsplit(as.character(lines[1,]),"")))
> changes first row to numeric vector.
>
>
Do I still need to loop through all lines?
It is maybe even slower now.

numbers <- vector('numeric')
for (i in 1:nrows(lines)) {
  numbers <- c(numbers, as.numeric(unlist(strsplit(as.
character(lines[i,]),""))))
}


> Anyway, can you explain what is your final goal?
>
>
A numeric vector of length 1 million. Each element should be one digit.


> Cheers
> Petr
>
>
Thanks.
/Martin

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: Optimize code to read text-file with digits

Peter Dalgaard-2
In reply to this post by Martin Møller Skarbiniks Pedersen
Simplest version that I can think of:

x <- scan("~/Downloads/digits.txt")
x <- x[-seq(1,220000,11)]
length(x) # 200000
hist(x)

Now, because it's Friday:

How does one work out the theoretical distribution of the following table?

> table(table(factor(x,levels=0:99999)))

    0     1     2     3     4     5     6     7     8     9    10    11
13497 27113 27010 18116  9122  3466  1186   366    99    22     1     1
   12
    1

(I.e., out of 200000 random 5 digit numbers, 13497 numbers never occurred, 27113 numbers exactly once, and ... and 1 number occurred 12 times.)

-pd


> On 8 Sep 2017, at 10:48 , Martin Møller Skarbiniks Pedersen <[hidden email]> wrote:
>
> Hi,
>
>  Every day I try to write some small R programs to improve my R-skills.
>  Yesterday I wrote a small program to read the digits from "A Million
> Random Digits" from RAND.
>  My code works but it is very slow and I guess the code is not optimal.
>
> The digits.txt file downloaded from
> https://www.rand.org/pubs/monograph_reports/MR1418.html
> contains 20000 lines which looks like this:
> 00000   10097 32533  76520 13586  34673 54876  80959 09117  39292 74945
> 00001   37542 04805  64894 74296  24805 24037  20636 10402  00822 91665
> 00002   08422 68953  19645 09303  23209 02560  15953 34764  35080 33606
> 00003   99019 02529  09376 70715  38311 31165  88676 74397  04436 27659
> 00004   12807 99970  80157 36147  64032 36653  98951 16877  12171 76833
>
> My program which is slow looks like this:
>
> filename <- "digits.txt"
> lines <- readLines(filename)
>
> numbers <- vector('numeric')
> for (i in 1:length(lines)) {
>
>    # remove first column
>    lines[i] <- sub("[^ ]+ +","",lines[i])
>
>    # remove spaces
>    lines[i] <- gsub(" ","",lines[i])
>
>    # split the characters and convert them into numbers
>    numbers <- c(numbers,as.numeric(unlist(strsplit(lines[i],""))))
> }
>
> Thanks for any advice how this program can be improved.
>
> Regards
> Martin M. S. Pedersen
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: [hidden email]  Priv: [hidden email]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: Optimize code to read text-file with digits

PIKAL Petr
In reply to this post by Martin Møller Skarbiniks Pedersen
Hi

see in line


> -----Original Message-----
> From: R-help [mailto:[hidden email]] On Behalf Of Martin
> Moller Skarbiniks Pedersen
> Sent: Friday, September 8, 2017 11:58 AM
> To: [hidden email]
> Subject: Re: [R] Optimize code to read text-file with digits
>
> On 8 September 2017 at 11:25, PIKAL Petr <[hidden email]> wrote:
>
> > > Moller Skarbiniks Pedersen
>
> > My program which is slow looks like this:
> > >
> > > filename <- "digits.txt"
> > > lines <- readLines(filename)
> >
> > why you do not read a file as a whole e.g. by
> >
> > lines<-read.table("digits.txt")
> >
>
> Good idea.
>
> >
> > And now I am lost.
>
>
> [...]
>
>
> >  Or do you want one big numeric vector from all your numbers?
>
> here you need to read values as character variables
> >
>
> Yes. That's what I am looking for.

*********************

Well, this is how you cen get your numeric vector of length 1e6

set.seed(111)
numbers0<-sample(0:9, 1e6, replace=TRUE)

If you want to get this number vector from the file it is better to use lists and lapply but maybe with loop it can be done too

First I prepare some data>

daf<-as.character(numbers0)
index<- 0:(1e6-1)
index<-index%/%5
lll<-split(daf, index)
lll<-lapply(lll, paste, collapse="")
daf<-do.call(rbind, lll)
dim(daf)<-c(20000,10)
daf<-as.data.frame(daf)

# here we have data frame similar to what you can get with read.table
head(daf)
     V1    V2    V3    V4    V5    V6    V7    V8    V9   V10
1 57353 75381 66866 52351 03707 13763 76897 67383 02972 37636
2 40540 52811 02521 18199 23236 64967 70123 46962 95347 47379
3 55001 55094 36922 08811 77704 99060 65902 28279 29131 98979
4 41936 77976 71345 84996 36865 11825 11024 90616 35653 10772
5 42339 89821 23790 62176 03266 36054 34882 06822 10087 05317
6 36275 45199 80796 54458 38836 87953 64394 02685 25788 19502
>
# now it is time transform data.frame to numeric vector
# Change to list, transform to character, split to items, unlist and make numeric
lll<- as.list(daf)
lll<-lapply(lll, as.character)
numbers<-lapply(lll, strsplit,"")
numbers <- as.numeric(unlist(numbers))
length(numbers)
[1] 1000000
> all.equal(numbers, numbers0)
[1] TRUE
>
all this is computed in less than 1 second, is it really so slow?

Cheers
Petr

******************


>
> >
> > lines<-read.table("digits.txt", colClasses="character")
> > numbers<-as.numeric(unlist(strsplit(as.character(lines[1,]),"")))
> > changes first row to numeric vector.
> >
> >
> Do I still need to loop through all lines?
> It is maybe even slower now.
>
> numbers <- vector('numeric')
> for (i in 1:nrows(lines)) {
>   numbers <- c(numbers, as.numeric(unlist(strsplit(as.
> character(lines[i,]),""))))
> }
>
>
> > Anyway, can you explain what is your final goal?
> >
> >
> A numeric vector of length 1 million. Each element should be one digit.
>
>
> > Cheers
> > Petr
> >
> >
> Thanks.
> /Martin
>
>       [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

________________________________
Tento e-mail a jakékoliv k němu připojené dokumenty jsou důvěrné a jsou určeny pouze jeho adresátům.
Jestliže jste obdržel(a) tento e-mail omylem, informujte laskavě neprodleně jeho odesílatele. Obsah tohoto emailu i s přílohami a jeho kopie vymažte ze svého systému.
Nejste-li zamýšleným adresátem tohoto emailu, nejste oprávněni tento email jakkoliv užívat, rozšiřovat, kopírovat či zveřejňovat.
Odesílatel e-mailu neodpovídá za eventuální škodu způsobenou modifikacemi či zpožděním přenosu e-mailu.

V případě, že je tento e-mail součástí obchodního jednání:
- vyhrazuje si odesílatel právo ukončit kdykoliv jednání o uzavření smlouvy, a to z jakéhokoliv důvodu i bez uvedení důvodu.
- a obsahuje-li nabídku, je adresát oprávněn nabídku bezodkladně přijmout; Odesílatel tohoto e-mailu (nabídky) vylučuje přijetí nabídky ze strany příjemce s dodatkem či odchylkou.
- trvá odesílatel na tom, že příslušná smlouva je uzavřena teprve výslovným dosažením shody na všech jejích náležitostech.
- odesílatel tohoto emailu informuje, že není oprávněn uzavírat za společnost žádné smlouvy s výjimkou případů, kdy k tomu byl písemně zmocněn nebo písemně pověřen a takové pověření nebo plná moc byly adresátovi tohoto emailu případně osobě, kterou adresát zastupuje, předloženy nebo jejich existence je adresátovi či osobě jím zastoupené známá.

This e-mail and any documents attached to it may be confidential and are intended only for its intended recipients.
If you received this e-mail by mistake, please immediately inform its sender. Delete the contents of this e-mail with all attachments and its copies from your system.
If you are not the intended recipient of this e-mail, you are not authorized to use, disseminate, copy or disclose this e-mail in any manner.
The sender of this e-mail shall not be liable for any possible damage caused by modifications of the e-mail or by delay with transfer of the email.

In case that this e-mail forms part of business dealings:
- the sender reserves the right to end negotiations about entering into a contract in any time, for any reason, and without stating any reasoning.
- if the e-mail contains an offer, the recipient is entitled to immediately accept such offer; The sender of this e-mail (offer) excludes any acceptance of the offer on the part of the recipient containing any amendment or variation.
- the sender insists on that the respective contract is concluded only upon an express mutual agreement on all its aspects.
- the sender of this e-mail informs that he/she is not authorized to enter into any contracts on behalf of the company except for cases in which he/she is expressly authorized to do so in writing, and such authorization or power of attorney is submitted to the recipient or the person represented by the recipient, or the existence of such authorization is known to the recipient of the person represented by the recipient.
______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: Optimize code to read text-file with digits

Peter Dalgaard-2
In reply to this post by Peter Dalgaard-2

> On 8 Sep 2017, at 14:03 , peter dalgaard <[hidden email]> wrote:
>
> x <- scan("~/Downloads/digits.txt")
> x <- x[-seq(1,220000,11)]

...and, come to think of it, if you really want the 1000000 random digits:

xx <- c(outer(x,10^(0:4), "%/%")) %% 10

--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: [hidden email]  Priv: [hidden email]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: Optimize code to read text-file with digits

Martin Møller Skarbiniks Pedersen
On 8 September 2017 at 14:37, peter dalgaard <[hidden email]> wrote:

>
>
> > On 8 Sep 2017, at 14:03 , peter dalgaard <[hidden email]> wrote:
> >
> > x <- scan("~/Downloads/digits.txt")
> > x <- x[-seq(1,220000,11)]
>
> ...and, come to think of it, if you really want the 1000000 random digits:
>
> xx <- c(outer(x,10^(0:4), "%/%")) %% 10
>

Hi Peter,
  Thanks a lot for the answers. I can see that I need to read about outer().
  However I get a different result than expected.

R> x <- scan("digits.txt")
Read 220000 items

R> head(x)
[1]     0 10097 32533 76520 13586 34673

R> x <- x[-seq(1,220000,11)]
R> head(x)
[1] 10097 32533 76520 13586 34673 54876

R> head(c(outer(x,10^(0:4), "%/%")) %% 10, 10) #
[1] 7 3 0 6 3 6  9 7 2 5

Regards
Martin

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: Optimize code to read text-file with digits

Peter Dalgaard-2

> On 8 Sep 2017, at 15:51 , Martin Møller Skarbiniks Pedersen <[hidden email]> wrote:
>
> On 8 September 2017 at 14:37, peter dalgaard <[hidden email]> wrote:
>>
>>
>>> On 8 Sep 2017, at 14:03 , peter dalgaard <[hidden email]> wrote:
>>>
>>> x <- scan("~/Downloads/digits.txt")
>>> x <- x[-seq(1,220000,11)]
>>
>> ...and, come to think of it, if you really want the 1000000 random digits:
>>
>> xx <- c(outer(x,10^(0:4), "%/%")) %% 10
>>
>
> Hi Peter,
>  Thanks a lot for the answers. I can see that I need to read about outer().
>  However I get a different result than expected.
>
> R> x <- scan("digits.txt")
> Read 220000 items
>
> R> head(x)
> [1]     0 10097 32533 76520 13586 34673
>
> R> x <- x[-seq(1,220000,11)]
> R> head(x)
> [1] 10097 32533 76520 13586 34673 54876
>
> R> head(c(outer(x,10^(0:4), "%/%")) %% 10, 10) #
> [1] 7 3 0 6 3 6  9 7 2 5
>

Ah, right. You do get all the digits, but in the order of the last digit of each 5 digit number, then all the penultimate digits, etc. To get digits in the right order, try

> xx <- c(t(outer(x,10^(4:0), "%/%"))) %% 10
> head(xx, 100)
  [1] 1 0 0 9 7 3 2 5 3 3 7 6 5 2 0 1 3 5 8 6 3 4 6 7 3 5 4 8 7 6 8 0 9 5
 [35] 9 0 9 1 1 7 3 9 2 9 2 7 4 9 4 5 3 7 5 4 2 0 4 8 0 5 6 4 8 9 4 7 4 2
 [69] 9 6 2 4 8 0 5 2 4 0 3 7 2 0 6 3 6 1 0 4 0 2 0 0 8 2 2 9 1 6 6 5

I.e., reverse the order of digit generation and transpose the matrix that outer() creates (because matrices are column-major).



> Regards
> Martin
>
> [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: [hidden email]  Priv: [hidden email]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: Optimize code to read text-file with digits

Martin Maechler
>>>>> peter dalgaard <[hidden email]>
>>>>>     on Fri, 8 Sep 2017 16:12:21 +0200 writes:

    >> On 8 Sep 2017, at 15:51 , Martin Møller Skarbiniks
    >> Pedersen <[hidden email]> wrote:
    >>
    >> On 8 September 2017 at 14:37, peter dalgaard
    >> <[hidden email]> wrote:
    >>>
    >>>
    >>>> On 8 Sep 2017, at 14:03 , peter dalgaard
    >>>> <[hidden email]> wrote:
    >>>>
    >>>> x <- scan("~/Downloads/digits.txt") x <-
    >>>> x[-seq(1,220000,11)]
    >>>
    >>> ...and, come to think of it, if you really want the
    >>> 1000000 random digits:
    >>>
    >>> xx <- c(outer(x,10^(0:4), "%/%")) %% 10
    >>>
    >>
    >> Hi Peter, Thanks a lot for the answers. I can see that I
    >> need to read about outer().  However I get a different
    >> result than expected.
    >>
    R> x <- scan("digits.txt")
    >> Read 220000 items
    >>
    R> head(x)
    >> [1] 0 10097 32533 76520 13586 34673
    >>
    R> x <- x[-seq(1,220000,11)] head(x)
    >> [1] 10097 32533 76520 13586 34673 54876
    >>
    R> head(c(outer(x,10^(0:4), "%/%")) %% 10, 10) #
    >> [1] 7 3 0 6 3 6 9 7 2 5
    >>

    > Ah, right. You do get all the digits, but in the order of
    > the last digit of each 5 digit number, then all the
    > penultimate digits, etc. To get digits in the right order,
    > try

    >> xx <- c(t(outer(x,10^(4:0), "%/%"))) %% 10 head(xx, 100)
    >   [1] 1 0 0 9 7 3 2 5 3 3 7 6 5 2 0 1 3 5 8 6 3 4 6 7 3 5
    > 4 8 7 6 8 0 9 5 [35] 9 0 9 1 1 7 3 9 2 9 2 7 4 9 4 5 3 7 5
    > 4 2 0 4 8 0 5 6 4 8 9 4 7 4 2 [69] 9 6 2 4 8 0 5 2 4 0 3 7
    > 2 0 6 3 6 1 0 4 0 2 0 0 8 2 2 9 1 6 6 5

    > I.e., reverse the order of digit generation and transpose
    > the matrix that outer() creates (because matrices are
    > column-major).

As people are  "exercising" with R and it's Friday:

Try to use  read.fwf() instead of scan() to get to the digits directly,
and see if you get the identical digits, and if it is faster overall or not
[I have no idea of the answer to that].

another Martin.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Reply | Threaded
Open this post in threaded view
|

Re: Optimize code to read text-file with digits

R help mailing list-2
In reply to this post by Martin Møller Skarbiniks Pedersen
Remove the for loop and all the [i]'s in your code and it will probably go
faster.  I.e., change

f0 <- function (lines)
{
    numbers <- vector("numeric")
    for (i in 1:length(lines)) {
        lines[i] <- sub("[^ ]+ +", "", lines[i])
        lines[i] <- gsub(" ", "", lines[i])
        numbers <- c(numbers, as.numeric(unlist(strsplit(lines[i],
            ""))))
    }
    numbers
}

to

f1 <- function (lines)
{
    lines <- sub("[^ ]+ +", "", lines)
    lines <- gsub(" ", "", lines)
    as.numeric(unlist(strsplit(lines, "")))
}

I haven't measured it, but the big time sink may come from f0 growing the
'numbers' vector bit by bit.  That can cause a lot of reallocations and
garbage collections.

Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Fri, Sep 8, 2017 at 1:48 AM, Martin Møller Skarbiniks Pedersen <
[hidden email]> wrote:

> Hi,
>
>   Every day I try to write some small R programs to improve my R-skills.
>   Yesterday I wrote a small program to read the digits from "A Million
> Random Digits" from RAND.
>   My code works but it is very slow and I guess the code is not optimal.
>
> The digits.txt file downloaded from
> https://www.rand.org/pubs/monograph_reports/MR1418.html
> contains 20000 lines which looks like this:
> 00000   10097 32533  76520 13586  34673 54876  80959 09117  39292 74945
> 00001   37542 04805  64894 74296  24805 24037  20636 10402  00822 91665
> 00002   08422 68953  19645 09303  23209 02560  15953 34764  35080 33606
> 00003   99019 02529  09376 70715  38311 31165  88676 74397  04436 27659
> 00004   12807 99970  80157 36147  64032 36653  98951 16877  12171 76833
>
> My program which is slow looks like this:
>
> filename <- "digits.txt"
> lines <- readLines(filename)
>
> numbers <- vector('numeric')
> for (i in 1:length(lines)) {
>
>     # remove first column
>     lines[i] <- sub("[^ ]+ +","",lines[i])
>
>     # remove spaces
>     lines[i] <- gsub(" ","",lines[i])
>
>     # split the characters and convert them into numbers
>     numbers <- c(numbers,as.numeric(unlist(strsplit(lines[i],""))))
> }
>
> Thanks for any advice how this program can be improved.
>
> Regards
> Martin M. S. Pedersen
>
>         [[alternative HTML version deleted]]
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/
> posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

        [[alternative HTML version deleted]]

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.